[gmx-users] DNA simulations with GROMACS???

Anna Reymer anna.reymer at gmail.com
Tue Jun 26 16:59:04 CEST 2007


Hi!

Thank you all very much for the help!
The problem was in correct usage of water models.
I used amber_tip3p.gro and gromacs_tip3p.itp. So, it is necessary to
use both tip3p.gro and tip3p.itp from either amber or gromacs.

regards

/anna

On 6/19/07, Anna Reymer <anna.reymer at gmail.com> wrote:
> Hi again!
>
> The end of my top file looks :
> [ molecules ]
> ; Compound        #mols
> Protein             1
> SOL             10682
>
>
> /Anna
>
> On 6/19/07, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> >
> > 19 jun 2007 kl. 09.31 skrev Anna Reymer:
> >
> > > Dear GROMACS users!
> > >
> > > Is it possible to model DNA with the help of GROMACS with AMBER ports?
> > > I've checked mailing-list and found that the only GROMCAS force field
> > > appropriate for modeling DNA is OPLS, but it does not provide good
> > > enough results for long DNA MD runs.
> > > The mailing-list suggested AMBER ports. I've managed to produce
> > > topology and coordinates files, solvate the system. But when I came to
> > > grompp step, I got the following error message:
> > >
> > > Program grompp, VERSION 3.3.1
> > > Source code file: grompp.c, line: 448
> > >
> > > Fatal error:
> > > number of coordinates in coordinate file (genbox.gro, 32804)
> > >             does not match topology (dick.top, 0)
> > > ---
> > > I've checked my dick.top file and it looks OK. I've also checked
> > > ffamber99.rtp, ffamber99.atp, ffamber.hdb,ffamberbon.itp and several
> > > other files. I am not a programmer myself, but I checked the same sort
> > > of files for GROMOS force fields, they have different format and I
> > > suspect that this is the reason for the error message. The program
> > > simply can't parse some files.
> > > Has someone tried modelling DNA in GROMACS with AMBER ports? Was it
> > > successful?
> > > Thank you all in advance.
> > >
> >
> > I have, and it works just fine. I suspect there is indeed something
> > wrong with your top-file. Check your #includes. What does your
> > [ molecules ] section look like?
> >
> > /Erik
> > > regards,
> > > Anna
> > > _______________________________________________
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> > _______________________________________________
> > Erik Marklund, PhD student
> > Laboratory of Molecular Biophysics,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  75124 Uppsala, Sweden
> > phone:  +46 18 471 4537         fax: +46 18 511 755
> > erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
> >
> >
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